Hey!
I'm sorry to hear you lost your saved file, though it seems weird to me an rpg maker file gets deleted out of nowhere. I guess the best way to prevent losing saved files, would be either save on different save slots, or time to time backup the whole save folder (www/save) and if you happen to lost again another save file, you could take the singular saved file from the backup folder.
Hope this might help you and thank you for showing interest in this game!